Research workbench
Structural characterization of the fast and promiscuous macrocyclase from plant - PCY1-S562A bound to presegetalin B1
Analyse Structural characterization of the fast and promiscuous macrocyclase from plant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O3V
- Type
- protein
- Length
- 1,459 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide cyclase 1; Putative presegetalin B1
- UniProt
- R4P353, F6LNL6
- Ligands
- MG, SO4
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Peptide cyclase 1 | protein | 716 | 23% helix, 31% strand | R4P353 |
| D | Putative presegetalin B1 | protein | 14 | 0% helix, 0% strand | F6LNL6 |
| C | Putative presegetalin B1 | protein | 13 | 0% helix, 0% strand | F6LNL6 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.85 | 0.86 | 133 | empty |
| 2 | 864 | 0.84 | 0.86 | 92 | empty |
| 3 | 269 | 0.69 | 0.84 | 35 | empty |
| 4 | 283 | 0.68 | 0.83 | 34 | empty |
| 5 | 248 | 0.66 | 0.83 | 34 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1160 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1128 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 670 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5O3V · Structural characterization of the fast and promiscuous macrocyclase from plant… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt R4P353
- Every structure of UniProt F6LNL6
- Elsewhere: RCSB PDB 5O3V · PDBe 5O3V · UniProt R4P353 · UniProt F6LNL6
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